Workflow to get from FASTQ files to calling the HPV geno- and subtype, given references of possible types. The worfklow will also generate a report with nucleotide and amino acid changes. The algorithm VirStrain is used within the pipeline (https://github.com/liaoherui/VirStrain).
See FindHPVMutations_Manual_eng.odt for instructions